Release Schedule

We are interested in ideas/classes/code/etc. to be included in future Bioperl releases, specifically the next developer release (1.5.2), the next stable release (1.6), and beyond. Please keep the ideas/comments as short as possible, and leave a signature using '~~~~'. --Chris Fields 12:34, 8 August 2006 (EDT)

Use the discussion page for questions and answers. --Senduran 16:16, 14 August 2006 (EDT)

Split and rename related tests (SearchIO.t and hmmer.t, for instance) into smaller test files (SearchIO_blast.t, SearchIO_hmmer.t, SearchIO_infernal.t, etc). This same theme could be used for Bio::SeqIO, Bio::AlignIO, and other 'pluginable' parsers.

The tests should be as focused as possible, the end result hopefully being that these changes are geared towards...

post-1.6 releases when splitting up BioPerl into their respective smaller distributions, and...

will probably help tremendously when bugfixing, targeting modules for deprecation, etc.

Related to the above: we probably can group related tests with similar themes together (Variation_*.t, Coordinate_*.t, etc).

Bio::LocatableSeq has issues with translated nucleotide sequences derived from BLAST/FASTA reports. This has been partially fixed by using a mapping() method, but TFASTX/Y frameshifts aren't yet supported.

OTHER BUGS TO BE ADDED

The following are now pushed to later releases (the below are much easier to accomplish once we split bioperl into set subdistributions, so should wait until after 1.6):

Improve test coverage: try to ensure that all methods are fully tested in t/module.t

Reports which modules are complete and which are not

For incomplete or unmaintained modules introduced since 1.4, move, remove, or revert

What are the main impediments/issues we need to resolve for a 1.6 release?

Need tests

The existing tests were moved over to Bio::Root::Test which makes dealing with them easier, but they are still completely inadequate in terms of code coverage.

As I (Senduran) see it, we can't claim a 'stable' release by either sense of the word. We don't know if its sufficiently bug free, not has the API been given a thorough work-out to see if it makes enough sense for us to recommend and support it for years to come.

Moving toward complete test coverage will also make clear the modules that can't go into 1.6 because they're only partially developed or non-functional.

This is the major work that needs to be done vs. the 1.5.2 release, and it is a substantial job requiring organization and a dedicated team.

Not sure how feasible this is. It would be easier to vet modules when coming in, probably by pushing new ones into a separate 'dev' or 'extras' distribution prior to rigorous testing. --Chris Fields 13:15, 12 February 2008 (EST)

Tracking test coverage and splitting modules into groups will be a feature of the next release series of BioPerl. At this point we need to get a new release series out ASAP, then follow it up with regular bug-fix releases. Whether we stick with the 'stable' designation or not is up to debate. --Chris Fields 20:13, 30 July 2008 (UTC)